scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- Remove `sc.external`
- sc.pp.neighbors(..., knn=True, n_neighbors=k) does not threshold the adjacency
- Investigate Array API usage in scanpy codebase
- pbmc68k_reduced raw counts
- negative values after score_genes with log1P or counts layer
- rank_genes_groups logfoldchange different than seurat
- Fix paga root
- Allow using arbitrary vectors in plotting (not only `obs` columns)
- plotting by sc.pl.dpt_timeseries(adata) has no colors
- obs. vs. obs for all grouped plots using `BasePlot`
- Docs
- Python not yet supported